Use `openff-packmol` by mattwthompson · Pull Request #1423 · openforcefield/openff-interchange

mattwthompson · 2026-02-05T14:39:09Z

Description

Checklist

Add tests
Lint
Update docstrings

for more information, see https://pre-commit.ci

codecov · 2026-02-05T15:23:32Z

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❌ Patch coverage is 0% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 0.00%. Comparing base (cbc0179) to head (d68088a).
⚠️ Report is 3 commits behind head on main.

Files with missing lines	Patch %	Lines
openff/interchange/components/_packmol.py	0.00%	2 Missing ⚠️

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@@            Coverage Diff             @@
##             main   #1423       +/-   ##
==========================================
- Coverage   93.97%   0.00%   -93.98%     
==========================================
  Files          73      73               
  Lines        6340    6046      -294     
==========================================
- Hits         5958       0     -5958     
- Misses        382    6046     +5664

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mattwthompson · 2026-03-27T14:51:24Z

pixi.toml

 [feature.etc.dependencies]
 # a Packmol install separate from AmberTools is needed to test PBCs
-packmol = ">=20.15.0"
+openff-packmol = "*"


This is a slight-of-hand of complexity; AmberTools forbids Packmol from being installed alongside it, so this can only go into the Pixi feature I designed around not having AmberTools.

This ultimately needs to be dealt with at the packaging level

Wrote up here: conda-forge/openff-packmol-feedstock#1

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mattwthompson · 2026-03-30T14:45:50Z

Blocked by conda-forge/openff-packmol-feedstock#1

Copilot

Pull request overview

This PR migrates PACKMOL-related functionality in openff-interchange to use the external openff-packmol package, updating imports, environments, and CI configuration accordingly.

Changes:

Replaced the in-repo PACKMOL wrapper implementation with a re-export shim pointing to openff.packmol.
Updated Pixi environments/features and dependencies to install openff-packmol and (optionally) the packmol executable.
Updated tests and example notebooks to import PACKMOL utilities from openff.packmol instead of openff.interchange.components._packmol.

Reviewed changes

Copilot reviewed 11 out of 12 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
`pyproject.toml`	Adds `openff.packmol.*` to mypy ignored imports.
`pixi.toml`	Pins `openff-interchange-base` to `0.5.*`, adds `openff-packmol`, introduces a `packmol` feature group, and updates env definitions.
`openff/interchange/components/_packmol.py`	Replaces the local implementation with imports/re-exports from `openff.packmol._packmol`.
`openff/interchange/_tests/unit_tests/interop/openmm/_import/test_virtual_sites.py`	Switches `solvate_topology` import to `openff.packmol`.
`openff/interchange/_tests/unit_tests/components/test_packmol.py`	Removes the in-repo packmol unit test suite.
`openff/interchange/_tests/test_issues.py`	Switches PACKMOL-related imports to `openff.packmol`.
`openff/interchange/_tests/interoperability_tests/components/test_packmol.py`	Switches to `openff.packmol` (and `_find_packmol` from its private module).
`examples/protein_ligand/protein_ligand.ipynb`	Updates imports to use `openff.packmol`.
`examples/packed_box/packed_box.ipynb`	Updates imports to use `openff.packmol`.
`examples/ligand_in_water/ligand_in_water.ipynb`	Updates imports to use `openff.packmol`.
`.github/workflows/ci.yaml`	Removes `etc` environments from the matrix and enables Pixi frozen installs.

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Copilot · 2026-04-03T16:21:04Z

openff/interchange/components/_packmol.py

@@ -2,1161 +2,60 @@
 A wrapper around PACKMOL. Adapted from OpenFF Evaluator v0.4.3.


The module docstring is now misleading: this file no longer implements a Packmol wrapper (it re-exports symbols from openff-packmol). Please update the docstring to reflect that it’s a compatibility re-export (and, if intended, note any deprecation/migration guidance).

Suggested change

A wrapper around PACKMOL. Adapted from OpenFF Evaluator v0.4.3.

Compatibility re-export of PACKMOL utilities from ``openff.packmol._packmol``.

This module no longer implements the PACKMOL wrapper directly; it re-exports

symbols to preserve the historical import path. New code should prefer importing

from ``openff.packmol._packmol`` directly.

Copilot · 2026-04-03T16:21:04Z

openff/interchange/components/_packmol.py

+from openff.packmol._packmol import (
+    RHOMBIC_DODECAHEDRON,
+    RHOMBIC_DODECAHEDRON_XYHEX,
+    UNIT_CUBE,
+    _box_from_density,


This module imports everything from openff.packmol._packmol, which is a private (underscore-prefixed) module. Relying on private APIs increases the chance of breakage on openff-packmol updates; prefer importing from the public openff.packmol namespace (or add a small shim here that only depends on public exports).

Copilot · 2026-04-03T16:21:04Z

openff/interchange/_tests/interoperability_tests/components/test_packmol.py

 import pytest
+from openff.packmol import solvate_topology_nonwater
+from openff.packmol._packmol import _find_packmol
 from openff.toolkit import Quantity


The test now imports _find_packmol from openff.packmol._packmol, which is a private module. To reduce coupling to openff-packmol internals, consider using a public executable check (e.g., openff.utilities.has_executable("packmol") or shutil.which) for the skip condition instead of importing a private helper.

Copilot · 2026-04-03T16:21:05Z

pixi.toml

 nglview = "*"
 jax = "*"
 pyedr = "*"
-openff-nagl-base = "*"
+openff-nagl-base = ">=0.5.2"
 openff-nagl-models = "*"
+openff-packmol = "*"
+# smirnoff-plugins = "2025.*"  # https://github.com/conda-forge/smirnoff-plugins-feedstock/pull/23


openff.interchange.components._packmol now imports openff.packmol, but openff-packmol is only listed under the test feature dependencies here. If this module is part of the supported runtime API, consider moving openff-packmol into the base dependencies (or the packmol feature) so non-test environments that import it don’t fail.

Copilot · 2026-04-03T16:21:05Z

openff/interchange/components/_packmol.py

+__all__ = (
+    "RHOMBIC_DODECAHEDRON",
+    "RHOMBIC_DODECAHEDRON_XYHEX",
+    "UNIT_CUBE",
+    "_box_from_density",
+    "_box_vectors_are_in_reduced_form",
+    "_build_input_file",
+    "_center_topology_at",
+    "_check_add_positive_mass",
+    "_check_box_shape_shape",
+    "_compute_brick_from_box_vectors",
+    "_create_molecule_pdbs",
+    "_create_solute_pdb",
+    "_find_packmol",
+    "_get_packmol_version",
+    "_iter_lattice_vecs",
+    "_load_positions",
+    "_max_dist_between_points",
+    "_range_neg_pos",
+    "_scale_box",
+    "_unit_vec",
+    "_validate_inputs",
+    "_wrap_into",
+    "_wrap_into_brick",
+    "pack_box",
+    "solvate_topology",
+    "solvate_topology_nonwater",
 )


Since this file is now a compatibility re-export layer, it would be good to add/keep a small unit test that imports openff.interchange.components._packmol and asserts key symbols (e.g., pack_box, solvate_topology) are available. The previous packmol-specific unit tests were removed, so this backward-compatibility path is currently untested in this repo.

mattwthompson and others added 5 commits February 5, 2026 08:38

REF: Stage refactor to openff-packmol

11b07e3

MAINT: Update linters

c111727

Merge remote-tracking branch 'upstream/main' into new-packmol-wrapper

75c0236

[pre-commit.ci] auto fixes from pre-commit.com hooks

0679ed9

for more information, see https://pre-commit.ci

FIX: Fix imports

4ab1276

MAINT: Use new development tag

9d4fa06

jameseastwood assigned mattwthompson Feb 9, 2026

mattwthompson added 5 commits March 27, 2026 09:30

MAINT: Use released conda package

bbea930

Merge remote-tracking branch 'upstream/main' into new-packmol-wrapper

7105c05

Fix

2d5132e

Revert some changes

31d3164

Lint

95e97f4

mattwthompson commented Mar 27, 2026

View reviewed changes

mattwthompson added 2 commits March 27, 2026 09:56

Fix type-checking

24be24f

MAINT: More refactoring

deb44b3

mattwthompson changed the title ~~Stage refactor to openff-packmol~~ Use openff-packmol Mar 27, 2026

mattwthompson added 3 commits April 1, 2026 12:43

MAINT: Decouple Packmol and openff-packmol

830ee76

MAINT: Dependency fixes

b7c31b1

MAINT: Drop un-used environments

18a0f8e

mattwthompson marked this pull request as ready for review April 3, 2026 16:14

mattwthompson requested a review from Copilot April 3, 2026 16:14

Copilot started reviewing on behalf of mattwthompson April 3, 2026 16:15 View session

Copilot AI reviewed Apr 3, 2026

View reviewed changes

mattwthompson added 2 commits April 3, 2026 14:54

MAINT: Update Pixi manifest

d048b1b

TST: Actually test re-export

d68088a

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		@@ -2,1161 +2,60 @@
		A wrapper around PACKMOL. Adapted from OpenFF Evaluator v0.4.3.

-A wrapper around PACKMOL. Adapted from OpenFF Evaluator v0.4.3.
+Compatibility re-export of PACKMOL utilities from ``openff.packmol._packmol``.
+This module no longer implements the PACKMOL wrapper directly; it re-exports
+symbols to preserve the historical import path. New code should prefer importing
+from ``openff.packmol._packmol`` directly.

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